AVWUTILS - Miscellaneous Image Utilities

AVWUTILS is a set of useful command-line utilities which allow the conversion, processing etc. of Analyze/AVW and Nifti format data sets. Many of them work on both 3D and 4D data. For each of these programs, type just the program name to get the usage help.

The different AVWUTILS programs are:

• avw2ascii - convert image files to ASCII text file (or files if data is 4D).
  
  
• avwcc - run cross-correlations between every volume in one 4D data set with every volume in another (for investigating similarities in ICA outputs).
  
  
• avwchfiletype - used to change the file type of an image (e.g. from ANALYZE_GZ to NIFTI). The first argument is the desired file type (one of ANALYZE, ANALYZE_GZ, NIFTI, NIFTI_GZ, NIFTI_PAIR, NIFTI_PAIR_GZ) and the second is the input file. If no third argument is given then the input file is converted in place. This in place conversion removes the original files: e.g. for an Analyze file called stdimg then avwchfiletype NIFTI_GZ stdimg would replace stdimg.hdr and stdimg.img with stdimg.nii.gz. Note that having multiple copies of an image with the same basename and different filetypes (e.g. stdimg.nii.gz and stdimg.hdr and stdimg.img) creates many problems for determining what images to read, and in general will cause FSL programs to stop.
  
  
• avwcomplex - a utility that allows 3D or 4D complex image files to be split or constructed from corresponding real components (either Cartesian or polar). The initial flag indicates what kind of processing is done. In addition, two optional arguments at the end specify the first and last 3D volumes to be processed when the input is 4D (default is to do all volumes).
  
  
• avwcpgeom - copy certain parts of the header information (image dimensions, voxel dimensions, voxel dimensions units string, image orientation/origin or qform/sform info) from one image to another. Note that only copies from Analyze to Analyze or Nifti to Nifti will work properly. Copying from different files will result in loss of information or potentially incorrect settings.
  
  
• avwcreatehd - creates a new image header along with a zero intensity data image. There are two forms of input: one takes a list of minimal information on the command line, the other takes in an xml-style file, as written by avwhd -x. The information required in the first version is: x/y/z/tsize for image dimensions, x/y/zvoxsize for voxel dimensions (eg in mm), tr for time between volumes (for 3D data set to 0), x/y/zorigin for co-ordinate origin (eg for Talairach space - otherwise leave as 0 0 0), datatype for the voxel data type (the commonest are: 1=binary, 2=unsigned char, 4=signed short, 8=signed int, 16=float). Note that this is different from the previous versions in that an entire image is created, and will overwrite any .img file contents of the same image name.
  
  
• avwedithd - allows the header information in and image to be edited in a text-based xml-style format (like the output of avwhd -x but with redundant fields removed and some help text provided). Note that the default text editor used is pico, but other editors can be specified by the second argument.
  
  
• avwfill - fill non-brain parts of a 4D data set with data copied from inside the brain and adjust time series accordingly - useful for programs which need a complete rectangular matrix filled with usable but null data.
  
  
• avwhd - report every field of an Analyze or Nifti header (note that the fields are different although some are common, e.g. pixdims). The option "-x" produces an xml-style output which can be used in conjunction with avwcreatehd.
  
  
• avwinterleave - interleave two inputs to form a combined image.
  
  
• avwmaths - simple but powerful program to allow mathematical manipulation of images.
  
  
• avwmerge - concatenate image files into a single output. This concatenation can be in time, or in X, Y or Z. All image dimensions (except for the one being concatenated over) must be the same in all input images. For example, this can be used to take multiple 3D files (eg as output by SPM) and create a single 4D image file.
  
  
• avwnvols - report how many time points are in the input 4D data set.
  
  
• avworient - reports or sets the left-right orientation information in a file. Note that only in Nifti files can the orientation be changed - Analyze files are always treated as radiological. Note that this command does not change the data storage at all - only the orientation information in the header.
  
  
• avwroi - extract region of interest (ROI) from an image. You can a) take a 3D ROI from a 3D data set (or if it is 4D, the same ROI is taken from each time point and a new 4D data set is created), b) extract just some time points from a 4D data set, or c) control time and space limits to the ROI.
  
  
• avwsplit - split a 4D file into lots of 3D files (eg for inputting to SPM).
  
  
• avwstats - report certain summary statistics for an input 3D/4D image. Of particular value is the "robust intensity range" which calculates the 2% and 98% percentiles.
  
  
• avwstats++ - just like avwstats but can also calculate percentiles (e.g. p 50 gives the median), and the centre of gravity. In addition, it can take an aribitrary mask as input so that statistics are only calculated within the mask.
  
  
• avwswapdim - re-orders the data storage to permit changes between axial, saggital and coronal slicing. It can also be used to swap the left-right order of the data, but will not change the left-right orientation information in the header. Therefore after swapping left-right (e.g. using -x y z as arguments) the viewed image will be different. If the header information is also swapped (by using avworient) then the image will display as it originally did, although the data will be stored in a different order. This command is recommended for changing neurologically-ordered data into radiologically-ordered data.
  
  
• avwval - report a particular parameter (given a particular keyword eg "dim4") from an image header. To see the list of keywords run avwhd on the header and look at the first column.

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• avwfixfloat - sets all non-finite (NaN, Inf) values and very small values (<1e-37) to zero, which helps avoid some floating point errors on Alpha machines. Note that this is only works for volumes with data type = float.
  
  
• if2avw - convert some Interfile format images to Analyze or Nifti. This is nowhere near a complete implementation so beware!